rs4054823

chr17-13721707-T-Cchr17-13721707-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.426 in 151,954 control chromosomes in the GnomAD database, including 14,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64739 AN: 151836 Hom.: 14130 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.426 AC: 64789 AN: 151954 Hom.: 14141 Cov.: 32 AF XY: 0.431 AC XY: 31998 AN XY: 74264

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.421

Alfa AF: 0.449 Hom.: 21867

Bravo AF: 0.419

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
Cadd	Benign	22
Dann	Benign	0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4054823; hg19: chr17-13625024;